Calculation of effective reproduction number (R effective) using
rolling average
Only include cases > 5 (otherwise huge R)
R package: EpiEstim
Weekly data, not daily
serial interval—the time from illness onset in a primary case
(infector) to illness onset in a secondary case (infectee)
Mean and standard deviation of the serial interval = 1 week, but
maybe = 3 days, sd= 1 days would be better
But I cannot define values < 1, e.g 3/7
However, 1 week is not that bad as assumption for “mean serial
interval” (e.g. SARS 8.4 days, first SARS-COV-2 estimations 7.8 days,
later studies 4 days)
R effective estimated with 3 weeks -> R effect with weekly data?
Possible? Not too much noise?
Maps - Municipalities
calculated only for pandemic times:
28.06.1918 - 20.06.1919
09.01.1920 - 18.06.1920
06.01.1922 - 21.04.1922
04.01.1924 - 06.06.1924
b1.11.1924 - 08.05.1925
Incidence:
breaks: Jenks Natural Breaks - finds the “best” way to split up the
ranges.
natural breaks minimizes the variation within each color, so the
areas within each color are as close as possible in value to each
other
quantile breaks do not work, because there are many zeros in the
municipalities from 1920 onwards
Hotspots:
local spatial statistic G
R package: spdep
returned is a Z-value
high positive values indicate the posibility of a local cluster of
high values
low relative values a similar cluster of low values
